PXD018943

PXD018943 is an original dataset announced via ProteomeXchange.

Title	Chromosome-level de novo assembly and annotation of pig-tailed (macaca nemestrina) macaque genome
Description	Macaque species share over 93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g.,HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort. To close this gap and enhance functional genomics approaches, we employed a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome-level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells (iPSCs) derived from the same animal. Reconstruction of the evolutionary tree using whole genome annotation and orthologous comparisons among three macaque species, human and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques. These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.
HostingRepository	PRIDE
AnnounceDate	2020-05-04
AnnouncementXML	Submission_2020-05-04_09:34:43.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD018943
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Morteza Roodgar
SpeciesList	scientific name: Macaca nemestrina; NCBI TaxID: 9545;
ModificationList	Oxidation; Acetyl; Carbamidomethyl; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-01 01:07:04	ID requested
⏵ 1	2020-05-04 09:34:44	announced

Dataset with its publication pending

submitter keyword: Pig-tailed macaque, genome, assembly. proteomics

Michael P. Snyder
contact affiliation	Professor and Chair, Stanford Department of Genetics
contact email	mpsnyder@stanford.edu
lab head
Morteza Roodgar
contact affiliation	Stanford University, Department of Genetics
contact email	mroodgar@stanford.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD018943
     1. Label: PRIDE project
     2. Name: Chromosome-level de novo assembly and annotation of pig-tailed (macaca nemestrina) macaque genome